Fixed upload metadata

openeogeotrellis/deploy/batch_job.py

@@ -270,6 +270,7 @@ def run_job(
 ):
     result_metadata = {}
 
+    stac_hrefs = []
     try:
         # We actually expect type Path, but in reality paths as strings tend to
         # slip in anyway, so we better catch them and convert them.
@@ -362,7 +363,7 @@ def run_job(
             ml_model_metadata=ml_model_metadata,
         )
         # perform a first metadata write _before_ actually computing the result. This provides a bit more info, even if the job fails.
-        write_metadata({**result_metadata, **_get_tracker_metadata("")}, metadata_file, job_dir)
+        write_metadata({**result_metadata, **_get_tracker_metadata("")}, metadata_file)
 
         for result in results:
             result.options["batch_mode"] = True
@@ -464,7 +465,7 @@ def run_job(
             ml_model_metadata=ml_model_metadata,
         )
 
-        write_metadata({**result_metadata, **_get_tracker_metadata("")}, metadata_file, job_dir)
+        write_metadata({**result_metadata, **_get_tracker_metadata("")}, metadata_file)
         logger.debug("Starting GDAL-based retrieval of asset metadata")
         result_metadata = _assemble_result_metadata(
             tracer=tracer,
@@ -483,18 +484,18 @@ def run_job(
 
         assert len(results) == len(assets_metadata)
         for result, result_assets_metadata in zip(results, assets_metadata):
-            _export_to_workspaces(
+            stac_hrefs += _export_to_workspaces(
                 result,
                 result_metadata,
                 result_assets_metadata=result_assets_metadata,
                 job_dir=job_dir,
                 remove_exported_assets=job_options.get("remove-exported-assets", False),
             )
     finally:
-        write_metadata({**result_metadata, **_get_tracker_metadata("")}, metadata_file, job_dir)
+        write_metadata({**result_metadata, **_get_tracker_metadata("")}, metadata_file, stac_hrefs)
 
 
-def write_metadata(metadata, metadata_file, job_dir: Path):
+def write_metadata(metadata, metadata_file, stac_hrefs: List[Union[str, Path]] = None):
     with open(metadata_file, 'w') as f:
         json.dump(metadata, f, default=json_default)
     add_permissions(metadata_file, stat.S_IWGRP)
@@ -508,16 +509,12 @@ def write_metadata(metadata, metadata_file, job_dir: Path):
             bucket = os.environ.get('SWIFT_BUCKET')
             s3_instance = s3_client()
 
-            paths = list(filter(lambda x: x.is_file(), job_dir.rglob("*")))
+            paths = [metadata_file] + (stac_hrefs or [])
+            # asset files are already uploaded by Scala code
             logger.info(f"Writing results to object storage. paths={paths}")
             for file_path in paths:
-                # TODO: Get list of files to upload from metadata file.
-                #  AFAIK, nothing else is created locally and needs to be uploaded to s3 afterwards.
-                if UDF_PYTHON_DEPENDENCIES_FOLDER_NAME in str(file_path):
-                    logger.warning(f"Omitting {file_path} as the executors will not be able to access it")
-                else:
-                    full_path = str(file_path.absolute())
-                    s3_instance.upload_file(full_path, bucket, full_path.strip("/"))
+                file_path = urlparse(str(file_path)).path
+                s3_instance.upload_file(file_path, bucket, file_path.strip("/"))
         else:
             _convert_job_metadatafile_outputs_to_s3_urls(metadata_file)
 
@@ -588,6 +585,7 @@ def _export_to_workspaces(
 
         if alternate:
             result_metadata["assets"][asset_key]["alternate"] = alternate
+    return stac_hrefs
 
 
 def _export_to_workspace(job_dir: str, source_uri: str, target: Workspace, merge: str, remove_original: bool) -> str:

tests/test_batch_result.py

@@ -1286,15 +1286,16 @@ def write_line(message):
             job_dir_files_s3 = [
                 o["Key"] for o in s3_instance.list_objects(Bucket=get_backend_config().s3_bucket_name)["Contents"]
             ]
-            assert job_dir_files_s3 == ListSubSet(
-                [
-                    f"{merge}/collection.json",
-                    f"{merge}/folder1/lon.tif",
-                    f"{merge}/folder1/lon.tif.json",
-                    f"{merge}/lat.tif",
-                    f"{merge}/lat.tif.json",
-                ]
-            )
+            for prefix in [merge, tmp_path.relative_to("/")]:
+                assert job_dir_files_s3 == ListSubSet(
+                    [
+                        f"{prefix}/collection.json",
+                        f"{prefix}/folder1/lon.tif",
+                        f"{prefix}/folder1/lon.tif.json",
+                        f"{prefix}/lat.tif",
+                        f"{prefix}/lat.tif.json",
+                    ]
+                )
 
         else:
             workspace_dir = Path(f"{workspace.root_directory}/{merge}")